% Generated by roxygen2: do not edit by hand

% Please edit documentation in R/custom_likelihoods.R

\name{custom_likelihoods}

\alias{custom_likelihoods}

\alias{print.custom_likelihoods}

\title{Customise likelihood functions for outbreaker}

\usage{

custom_likelihoods(...)

\method{print}{custom_likelihoods}(x, ...)

}

\arguments{

\item{...}{a named list of functions, each computing a log-likelihood component.}

\item{x}{an \code{outbreaker_config} object as returned by \code{create_config}.}

}

\value{

A named list of list(function, arity) pairs with the class

    \code{custom_likelihood}, each function implementing a customised

    log-likelihood component of outbreaker. Functions which are not

    customised will result in a list(NULL, 0) component. Any function with

    arity 3 must have the third parameter default to NULL.

a list of named functions

}

\description{

This function is used to specify customised likelihood functions for

outbreaker. Custom functions are specified as a named list or series of

comma-separated, named arguments, indicating which log-likelihood component

they compute. Values currently available are:

}

\details{

\itemize{

\item \code{genetic}: the genetic likelihood; by default, the function

\code{cpp_ll_genetic} is used.

\item \code{timing_sampling}: the likelihood of sampling times; by default, the function

\code{cpp_ll_timing_sampling} is used.

\item \code{timing_infections}: the likelihood of infection times; by default, the function

\code{cpp_ll_timing_infections} is used.

\item \code{reporting}: the likelihood of the reporting process; by default,

the function \code{cpp_ll_reporting} is used.

\item \code{contact}: the likelihood of the contact tracing data; by default,

the function \code{cpp_ll_contact} is used.

}

All log-likelihood functions should have the following arguments, in this

order:

\itemize{

\item \code{data}: a list of named items containing input data as returned by

\code{\link{outbreaker_data}}

\item \code{param}: a list of parameters with the class

\code{\link{create_param}}

}

}

\examples{

## specify a null model by disabling all likelihood components

f_null <- function(data, param) {

  return(0.0)

}

null_model <- custom_likelihoods(genetic = f_null,

                                timing_sampling = f_null,

                                timing_infections = f_null,

                                reporting = f_null,

                                contact = f_null)

null_config <- list(find_import = FALSE,

                    n_iter = 100,

                    sample_every = 1)

## load data

x <- fake_outbreak

data <- outbreaker_data(dates = x$sample, dna = x$dna, w_dens = x$w)

res_null <- outbreaker(data = data,

                       config = null_config,

                       likelihoods = null_model)

## visualise ancestries to see if all transmission trees have been explored

plot(res_null, type = "alpha")

}

\seealso{

See \href{http://www.repidemicsconsortium.org/outbreaker2/articles/customisation.html#customizing-likelihood}{customization vignette} for detailed examples on how to customize likelihoods.

}

\author{

Thibaut Jombart (\email{thibautjombart@gmail.com})

}